As far as I could figure this one out, U1 uploads the smallest files first to shrink the queue of pending files as fast as possible. You can monitor this using a terminal and type:
while true; do u1sdtool --waiting|wc -l; sleep 20;done
That will give you a neat integer with number of files left.
The "ubuntu notification" you get in the top right corner, which says that the same file is being uploaded is just presenting the first file on the list - and since your list might contain several large files - then that largest file may be the same number one on the list for quite some time.
If the number of files does not reduce itself then i'd recommend make an assessment: If your files are very large then compute the expected time (filesize/bandwidth), and if you think that this has passed hours ago, then restart the sync service using:
u1sdtool --disconnect; u1sdtool --connect
Then rerun the code (top) to monitor whether the number of files are reducing.